The X-ray structure of ferric Escherichia coli flavohemoglobin reveals an unespected geometry of the distal heme pocket

Experimental Data Snapshot

  • Resolution: 2.19 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 

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The X-Ray Structure of Ferric Escherichia Coli Flavohemoglobin Reveals an Unexpected Geometry of the Distal Heme Pocket

Ilari, A.Bonamore, A.Farina, A.Johnson, K.A.Boffi, A.

(2002) J Biol Chem 277: 23725

  • DOI: https://doi.org/10.1074/jbc.M202228200
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    The x-ray structure of ferric unliganded lipid-free Escherichia coli flavohemoglobin has been solved to a resolution of 2.2 A and refined to an R-factor of 19%. The overall fold is similar to that of ferrous lipid-bound Alcaligenes eutrophus flavohemoglobin with the notable exception of the E helix positioning within the globin domain and a rotation of the NAD binding module with respect to the FAD-binding domain accompanied by a substantial rearrangement of the C-terminal region. An inspection of the heme environment in E. coli flavohemoglobin reveals an unexpected architecture of the distal pocket. In fact, the distal site is occupied by the isopropyl side chain Leu-E11 that shields the heme iron from the residues in the topological positions predicted to interact with heme iron-bound ligands, namely Tyr-B10 and Gln-E7, and stabilizes a pentacoordinate ferric iron species. Ligand binding properties are consistent with the presence of a pentacoordinate species in solution as indicated by a very fast second order combination rates with imidazole and azide. Surprisingly, imidazole, cyanide, and azide binding profiles at equilibrium are not accounted for by a single site titration curve but are biphasic and strongly suggest the presence of two distinct conformers within the liganded species.

  • Organizational Affiliation

    CNR Center of Molecular Biology and the Department of Biochemical Sciences, University of La Sapienza, 00185 Rome, Italy.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
FLAVOHEMOPROTEIN396Escherichia coliMutation(s): 0 
Find proteins for P24232 (Escherichia coli (strain K12))
Explore P24232 
Go to UniProtKB:  P24232
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP24232
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 2.19 Å
  • R-Value Free: 0.247 
  • R-Value Work: 0.187 
  • R-Value Observed: 0.187 
  • Space Group: P 6 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 164.86α = 90
b = 164.86β = 90
c = 53.46γ = 120
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-08-06
    Type: Initial release
  • Version 1.1: 2011-05-08
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-05-08
    Changes: Data collection, Database references, Derived calculations, Other